Closed logstar closed 1 year ago
Hi @kelseykeith . Thank you for reviewing the PR.
I was wondering if the lsb-release
issue could be addressed in a separate issue/PR. The current v12 final-release database was built on an ubuntu EC2 instance without installing lsb-release
in the db/build_tools/build_db.Dockerfile
. The lsb-release
error might need to be reproduced with major changes to the local v12 final-release database building environment, such as docker version, docker image version, and operating system version. The local building environment changes might cause additional dependency issues. Therefore, I was wondering if it might be more efficient to resolve the lsb-release
issue in a standalone PR, or a PR that starts development with the lsb-release
installed.
Yes, I'm fine with that. I can either submit a standalone PR for the issue or include it with my CNV database PR once we get there
Thank you. I will also add lsb-release
installation to the db/build_tools/build_db.Dockerfile
before working on the next issue.
I will merge this PR soon to update the QA API site.
Updated API database using OpenPedCan-analysis v12 final release data. The following filtered files in
s3://d3b-openaccess-us-east-1-prd-pbta/open-targets/v12/api-data/
were used for building the API database:efo-mondo-map.tsv
ensg-hugo-pmtl-mapping.tsv
gene-counts-rsem-expected_count-collapsed-deseq.rds
The filtered files were generated by the
filter-mtp-tables
module in the OpenPedCan-analysis.Resolved #86
Type of change
Changed
OpenPedCan-analysis
v12 final release data.db/build_db.sh
to download OpenPedCan-analysisapi-data
usingdb/build_tools/download_api_data.sh
.db/build_tools/build_db_docker_cmd.sh
to compress intermediate CSV files.Added
db/build_tools/download_api_data.sh
to download OpenPedCan-analysisapi-data
.How Has This Been Tested?
Terminal returns for testing DEV host:
For more details about testing environment, options, and resources, see
README.md
.Checklist